In the deep ocean, these bacteria play a key role in trapping carbon

A mysterious group of microbes may be controlling the fate of carbon in the dark depths of the world’s oceans.

Nitrospinae bacteria, which use the nitrogen compound nitrite to “fix” inorganic carbon dioxide into sugars and other compounds for food and reproduction, are responsible for 15 to 45 percent of such carbon fixation in the western North Atlantic Ocean, researchers report in the Nov. 24 Science. If these microbes are present in similar abundances around the world — and some data suggest that the bacteria are — those rates may be global, the team adds.

The total amount of carbon that Nitrospinae fix is small when compared with carbon fixation on land by organisms such as plants or in the sunlit part of the ocean, says Maria Pachiadaki, a microbial ecologist at Bigelow Laboratory for Ocean Sciences in East Boothbay, Maine, who is lead author on the new study. “But it seems to be of major importance to the productivity and health of the 90 percent of the ocean that is too deep and too dark for photosynthesis.” These bacteria likely form the base of the food web in much of this enigmatic realm, she says.

Oceans cover more than two-thirds of Earth’s surface, and most of those waters are in the dark. In the shallow, sunlit part of the ocean, microscopic organisms called phytoplankton fix carbon dioxide through photosynthesis. But in the deep ocean where sunlight doesn’t penetrate, microbes that use chemical energy derived from compounds such as ammonium or hydrogen sulfide are the engines of that part of the carbon cycle.

Little has been known about which microbes are primarily responsible for this dark ocean carbon fixation. The likeliest candidates were a group of ammonium-oxidizing archaea (single-celled organisms similar to bacteria) known as Thaumarchaeota because they are the most abundant microbes in the dark ocean.

But there was no direct proof that these archaea are the main fixers in those waters, says Pachiadaki. In fact, previous studies of carbon fixation in these depths suggested that ammonium-oxidizers weren’t performing the task quickly enough to match observations, she says. “The energy gained from ammonium oxidation is not enough to explain the amount of the carbon fixed in the dark ocean.”

She and colleagues suspected that a different group of microbes might be bearing the brunt of the task. Nitrospinae bacteria that use the chemical compound nitrite were known to be abundant in at least some parts of the dark ocean, but the microbes weren’t well studied. So Pachiadaki’s team analyzed 3,463 genomes, or genetic blueprints, of single-celled organisms found in 39 seawater samples collected in the western North Atlantic Ocean, at depths ranging from “twilight” regions below about 200 meters to the ocean’s deepest zone below 9,000 meters. The team identified Nitrospinae as the most abundant bacteria, particularly in the twilight zone. Although still less abundant than the ammonium-oxidizing Thaumarchaeota, the nitrite-oxidizers are much more efficient at fixing carbon, requiring only a tiny amount of available nitrite.

And although scientists knew that these bacteria use nitrite to produce energy, the new study showed that the compound is the primary source of energy for the microbes. Marine microbiologist Frank Stewart of Georgia Tech in Atlanta says the study “exemplifies how advances in genomic methods can generate hypotheses about metabolism and ecology.” These findings suggest that scientists need to rethink how energy and materials cycle in the dark ocean, he says. “While this ocean realm remains underexplored, studies like this are models for how to close our knowledge gap.”